3D nano-scale manufacturing is an important aspect of advanced manufacturing technology. A key element in ability to view, fabricate, and in some cases operate micro-devices is the availability of tightly focused particle beams, particularly of photons, electrons, and ions. The use of ions is the only way to fabricate directly micro-/ nano-scale structures. It has been utilized as a direct-write method for lithography, implantation, and milling of functional devices. The simulation of ion beam induced physical and chemical phenomena based on sound mathematical models associated with simulation methods is presented for 3D micro-/nanofabrication. The results obtained from experimental investigation and characteristics of ion beam induced direct fabrication will be discussed.